Manual

Package pymice

A collection of tools to access IntelliCage data.

class pymice.Loader(fname, getNp=True, getLog=False, getEnv=False, getHw=False, verbose=False, **kwargs)
__init__(fname, getNp=True, getLog=False, getEnv=False, getHw=False, verbose=False, **kwargs)
Parameters:
  • fname (basestring) – a path to the data file.
  • getNp (bool) – whether to load nosepoke data.
  • getLog (bool) – whether to load log.
  • getEnv (bool) – whether to load environmental data.
  • getHw (bool) – whether to load hardware data.
  • verbose (bool) – whether to output verbose messages
getVisits(mice=None, start=None, end=None, order=None)
Parameters:
  • mice (str or unicode or Animal or collection of them or None) – mouse (or mice) which visits are requested
  • start (datetime.datetime or None) – a lower bound of the visit Start attribute
  • end (datetime.datetime or None) – an upper bound of the visit Start attribute
  • order (str or unicode or their sequence or None) – attributes that the returned list is ordered by
Returns:

visits
Return type:

[Visit, ...]

 
>>> data.getVisits(mice='Mickey')
[< Visit of "Mickey" to corner #1 of cage #1 (at 2012-12-18 12:31:00.000) >]

>>> data.getVisits(mice=['Mickey', 'Minnie'], order='Start')
[< Visit of "Minnie" to corner #4 of cage #1 (at 2012-12-18 12:30:02.360) >,
 < Visit of "Mickey" to corner #1 of cage #1 (at 2012-12-18 12:31:00.000) >]

>>> mice = [data.getAnimal(m) for m in ['Mickey', 'Minnie']]
>>> data.getVisits(mice=mice, order='Start')
[< Visit of "Minnie" to corner #4 of cage #1 (at 2012-12-18 12:30:02.360) >,
 < Visit of "Mickey" to corner #1 of cage #1 (at 2012-12-18 12:31:00.000) >]
getLog(start=None, end=None, order=None)
Parameters:
  • start (datetime.datetime or None) – a lower bound of the log entries DateTime attribute
  • end (datetime.datetime or None) – an upper bound of the log entries DateTime attribute
  • order (str or unicode or their sequence or None) – attributes that the returned list is ordered by
Returns:

log entries
Return type:

[LogEntry, ...]

 
>>> data.getLog(order='DateTime')
[< Log Info, Application (at 2012-12-18 12:13:02.437) >,
 < Log Info, Application (at 2012-12-18 12:20:37.718) >]
getEnvironment(start=None, end=None, order=None)
Parameters:
  • start (datetime.datetime or None) – a lower bound of the sample DateTime attribute
  • end (datetime.datetime or None) – an upper bound of the sample DateTime attribute
  • order (str or unicode or their sequence or None) – attributes that the returned list is ordered by
Returns:

sampled environment conditions
Return type:

[EnvironmentalConditions, ...]

 
>>> data.getEnvironment(order=('DateTime', 'Cage'))
[< Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:13:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:13:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:14:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:14:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:15:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:15:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:16:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:16:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:17:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:17:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:18:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:18:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:19:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:19:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:20:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:20:02.000) >]
getHardwareEvents(start=None, end=None, order=None)
Parameters:
  • start (datetime.datetime or None) – a lower bound of the event DateTime attribute
  • end (datetime.datetime or None) – an upper bound of the event DateTime attribute
  • order (str or unicode or their sequence or None) – attributes that the returned list is ordered by
Returns:

hardware events
Return type:

[HardwareEvent, ...]
getAnimal(name=None)
Parameters:name (unicode convertable or None) – name of the animal
Returns:animal data if name given else names of animals
Return type:Animal if name given else frozenset([unicode, ...])
getCage(mouse)
Parameters:mouse (basestring or Animal) – mouse name or representation
Returns:cage(s) where mouse’s visits has been registered
Return type:convertable to int or (convertable to int, ..) 
>>> data.getCage('Minnie')
1

>>> data.getCage(data.getAnimal('Minnie'))
1
getInmates(cage=None)
Parameters:cage (convertable to int or None) – number of the cage
Returns:animals detected in the cage if given else available cages
Return type:frozenset(Animal, ...) if cage is given else frozenset(int, ...)
getGroup(name=None)
Parameters:name (basestring or None) – name of the group
Returns:group data if name given else names of groups
Return type:Group if name given else frozenset([unicode, ...])
getStart()
Returns:time of the earliest visit registration
Return type:datetime.datetime or None
getEnd()
Returns:time of the latest visit registration
Return type:datetime.datetime or None
class pymice.Merger(*dataSources, **kwargs)
>>> mm = Merger(ml_icp3, ml_l1)
>>> for v in mm.getVisits(order='Start'):
...   print('%s %d %s' % (str(v.Animal), len(v.Nosepokes), list(v.Animal.Tag)[0]))
Minnie 0 1337
Mickey 1 42
Jerry 2 69
Minnie 1 1337
Mickey 1 42
Jerry 2 69

>>> mm = Merger(ml_empty, ml_l1)
>>> for v in mm.getVisits(order='Start'):
...   print('%s %d' % (str(v.Animal), len(v.Nosepokes)))
Minnie 1
Mickey 1
Jerry 2

>>> mm = Merger(ml_retagged, ml_l1)
>>> for v in mm.getVisits(order='Start'):
...   print('%s %d' % (str(v.Animal), len(v.Nosepokes)))
...   print("  %s" % (', '.join(sorted(v.Animal.Tag))))
Mickey 0
  1337, 42
Minnie 1
  1337, 42
Jerry 2
  69
Minnie 1
  1337, 42
Mickey 1
  1337, 42
Jerry 2
  69
__init__(*dataSources, **kwargs)

Usage: Merger(data_1, [data_2, ...] [parameters])

Parameters:

dataSources ([Data, ...]) – objects containing IntelliCage data
Keyword Arguments:
 
  • getNp – whether to load nosepoke data (defaults to False).
  • getLog – whether to load log (defaults to False).
  • getEnv – whether to load environmental data (defaults to False).
  • getHw – whether to load hardware data (defaults to False).
  • ignoreMiceDifferences – whether to ignore encountered differences in animal description (e.g. sex)
getVisits(mice=None, start=None, end=None, order=None)
Parameters:
  • mice (str or unicode or Animal or collection of them or None) – mouse (or mice) which visits are requested
  • start (datetime.datetime or None) – a lower bound of the visit Start attribute
  • end (datetime.datetime or None) – an upper bound of the visit Start attribute
  • order (str or unicode or their sequence or None) – attributes that the returned list is ordered by
Returns:

visits
Return type:

[Visit, ...]

 
>>> data.getVisits(mice='Mickey')
[< Visit of "Mickey" to corner #1 of cage #1 (at 2012-12-18 12:31:00.000) >]

>>> data.getVisits(mice=['Mickey', 'Minnie'], order='Start')
[< Visit of "Minnie" to corner #4 of cage #1 (at 2012-12-18 12:30:02.360) >,
 < Visit of "Mickey" to corner #1 of cage #1 (at 2012-12-18 12:31:00.000) >]

>>> mice = [data.getAnimal(m) for m in ['Mickey', 'Minnie']]
>>> data.getVisits(mice=mice, order='Start')
[< Visit of "Minnie" to corner #4 of cage #1 (at 2012-12-18 12:30:02.360) >,
 < Visit of "Mickey" to corner #1 of cage #1 (at 2012-12-18 12:31:00.000) >]
getLog(start=None, end=None, order=None)
Parameters:
  • start (datetime.datetime or None) – a lower bound of the log entries DateTime attribute
  • end (datetime.datetime or None) – an upper bound of the log entries DateTime attribute
  • order (str or unicode or their sequence or None) – attributes that the returned list is ordered by
Returns:

log entries
Return type:

[LogEntry, ...]

 
>>> data.getLog(order='DateTime')
[< Log Info, Application (at 2012-12-18 12:13:02.437) >,
 < Log Info, Application (at 2012-12-18 12:20:37.718) >]
getEnvironment(start=None, end=None, order=None)
Parameters:
  • start (datetime.datetime or None) – a lower bound of the sample DateTime attribute
  • end (datetime.datetime or None) – an upper bound of the sample DateTime attribute
  • order (str or unicode or their sequence or None) – attributes that the returned list is ordered by
Returns:

sampled environment conditions
Return type:

[EnvironmentalConditions, ...]

 
>>> data.getEnvironment(order=('DateTime', 'Cage'))
[< Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:13:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:13:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:14:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:14:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:15:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:15:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:16:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:16:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:17:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:17:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:18:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:18:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:19:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:19:02.000) >,
 < Illumination:   0, Temperature: 22.0 (at 2012-12-18 12:20:02.000) >,
 < Illumination:   0, Temperature: 23.6 (at 2012-12-18 12:20:02.000) >]
getHardwareEvents(start=None, end=None, order=None)
Parameters:
  • start (datetime.datetime or None) – a lower bound of the event DateTime attribute
  • end (datetime.datetime or None) – an upper bound of the event DateTime attribute
  • order (str or unicode or their sequence or None) – attributes that the returned list is ordered by
Returns:

hardware events
Return type:

[HardwareEvent, ...]
getAnimal(name=None)
Parameters:name (unicode convertable or None) – name of the animal
Returns:animal data if name given else names of animals
Return type:Animal if name given else frozenset([unicode, ...])
getCage(mouse)
Parameters:mouse (basestring or Animal) – mouse name or representation
Returns:cage(s) where mouse’s visits has been registered
Return type:convertable to int or (convertable to int, ..) 
>>> data.getCage('Minnie')
1

>>> data.getCage(data.getAnimal('Minnie'))
1
getInmates(cage=None)
Parameters:cage (convertable to int or None) – number of the cage
Returns:animals detected in the cage if given else available cages
Return type:frozenset(Animal, ...) if cage is given else frozenset(int, ...)
getGroup(name=None)
Parameters:name (basestring or None) – name of the group
Returns:group data if name given else names of groups
Return type:Group if name given else frozenset([unicode, ...])
getStart()
Returns:time of the earliest visit registration
Return type:datetime.datetime or None
getEnd()
Returns:time of the latest visit registration
Return type:datetime.datetime or None

Auxilary tools

class pymice.Timeline(path, fname=None, tzinfo=None)

A class of objects for loading experiment timeline definition files.

As a subclass of matplotlib.ticker.Formatter the class is also time axis formatter in matplotlib.dates coordinates.

File format description

The format is a constrained INI format. Every section defined corresponds to phase of same name. The minimal information required about a phase are its boundaries given as start and end properties in format YYYY-MM-DD HH:MM or YYYY-MM-DD HH:MM:SS. Optional information about timezone of start and end properties might be provided by tzinfo property (name of timezone defined in pytz module).

New in version 1.0.0.

__init__(path, fname=None, tzinfo=None)

Read the description of the experiment timeline.

Parameters:
  • path (basestring) – a path to either the experiment timeline file or a directory containing experiment timeline file of either fname or ‘config.txt’ or ‘config*.(txt|ini)’ name (matching in that order).
  • fname (basestring or None) – name of the experiment timeline file in path directory
  • tzinfo (datetime.tzinfo) – default timezone
getTimeBounds(phases)
Parameters:phases ([basestring, ..] or basestring) – name(s) of phase(s)
Returns:timezone-aware boundaries of minimal period of time covering all phases given
Return type:(datetime.datetime, datetime.datetime)

New in version 1.0.0.

sections()

Return a list of section names, excluding [DEFAULT]

getTime()

Deprecated since version 1.0.0: Use getTimeBounds() instead.

class pymice.ExperimentTimeline

Deprecated since version 1.0.0: Use Timeline instead.

class pymice.DataValidator(*analyzers)

A class of objects performing data validation.

__init__(*analyzers)
Parameters:analyzers – a set of analyzers defining validation criteria
__call__(data)
Parameters:data (pymice.Data.Data) – data to be validated
Returns:description of data found invalid
Return type:(ExcludeMiceData, ...)
class pymice.LickometerLogAnalyzer(shortThreshold=3, medThreshold=None)

A class of objects detecting Lickometer type of warnings.

‘Lickometer is active but nosepoke is inactive’ errors might indicate a failure of the lickometer.

__init__(shortThreshold=3, medThreshold=None)
Parameters:
  • shortThreshold (int or float) – not used explicitly
  • medThreshold (int or float) – a maximal acceptable number of lickometer warnings within 1 hour bin; defaults to 4*``shortThreshold``
class pymice.PresenceLogAnalyzer

Class of objects validating data against ‘Presence’ warnings using a sophisticated heuristic.

The ‘Presence signal without antenna registration.’ warning might indicate that either an antenna is not working properly or a mouse has its transponder lost.

class pymice.FailureInspector(issue=None)

Class of objects for checking whether report generated by DataValidator objects confirms validity of given scope of data.

New in version 1.0.0.

__init__(issue=None)
Parameters:issue (basestring) – type of the invalidating issue
__call__(report, interval, **kwargs)
Parameters:
  • report (collection(ExcludeMiceData, ...)) – report generated by DataValidator
  • interval ((datetime.datetime, datetime.datetime)) – boundaries of temporal scope of validated data
Keyword Arguments:
 
  • cage – cage to which the scope of data is restricted
  • corner – corner to which the scope of data is restricted
  • side – side to which the scope of data is restricted
Returns:

True if the scope of data is valid else False
Return type:

bool
class pymice.TestMiceData

Deprecated since version 1.0.0: Use FailureInspector instead.

pymice.getTutorialData(path=None, quiet=False, fetch=None)

Write to disk example dataset(s) used in tutorials.

Parameters:
  • path (basestring) – a directory where tutorial data are to be loaded into (defaults to working directory)
  • quiet (bool) – a switch disabling stdout output.
  • fetch (collection(basestring, ..)) – the datasets to download
pymice.__PGP_PUBLIC_KEY__ = < ASCII armored PGP public key >

PGP public key for verifying of package updates from PyPI

class pymice.Citation(style=None, markdown=None, version='1.2.0', paperKey=None, softwareKey=None, **kwargs)

A class of objects facilitating referencing the PyMICE library.

Example:

>>> citation = Citation(version='1.1.1')
>>> print('''{reference}
... had no Citation class.
...
... Bibliography
...
... {reference.PAPER}
...
... {reference.SOFTWARE}
... '''.format(reference=citation))
PyMICE (Dzik, Puścian, et al. 2017) v. 1.1.1 (Dzik, Łęski, & Puścian 2017)
had no Citation class.

Bibliography

Dzik J. M., Puścian A., Mijakowska Z., Radwanska K., Łęski S. (June 22, 2017)
    "PyMICE: A Python library for analysis of IntelliCage data" Behavior
    Research Methods doi: 10.3758/s13428-017-0907-5

Dzik J. M., Łęski S., Puścian A. (April 24, 2017) "PyMICE" computer software
    (v. 1.1.1; RRID:nlx_158570) doi: 10.5281/zenodo.557087

New in version 1.2.0.

__init__(style=None, markdown=None, version='1.2.0', paperKey=None, softwareKey=None, **kwargs)
Keyword Arguments:
 
  • style – reference style; must be one of ‘PyMICE’, ‘APA6’, ‘Vancouver’, ‘BibTeX’; defaults to ‘PyMICE’
  • markdown – markdown language to be used; must be one of ‘txt’, ‘rst’, ‘md’, ‘html’, ‘LaTeX’; default value depends on the reference style
  • version – version of the PyMICE library to be referenced; None if no version shall be referenced; omit to reference the current version
  • paperKey – a key (e.g. LaTeX label or entry number) for the bibliography entry referencing the paper introducing the PyMICE library
  • softwareKey – a key (e.g. LaTeX label or entry number) for the bibliography entry referencing the PyMICE library

Warning

All constructor parameters shall be given as keyword arguments.

No undocumented parameter shall be used.

__str__()

Example:

>>> citation = Citation(version='1.1.1')
>>> print(str(citation))
PyMICE (Dzik, Puścian, et al. 2017) v. 1.1.1 (Dzik, Łęski, & Puścian 2017)
Returns:UTF-8 encoded recommended in-text reference
Return type:str
__unicode__()

Example:

>>> citation = Citation(version='1.1.1')
>>> print(unicode(citation))
PyMICE (Dzik, Puścian, et al. 2017) v. 1.1.1 (Dzik, Łęski, & Puścian 2017)
Returns:recommended in-text reference
Return type:unicode
cite(style=None, **kwargs)

Generete an in-text reference to the PyMICE library in the recommended format. Keyword attributes override parameters set in the object constructor.

Keyword Arguments:
 
  • style – reference style; must be one of ‘PyMICE’, ‘APA6’, ‘Vancouver’, ‘BibTeX’
  • markdown – markdown language to be used; must be one of ‘txt’, ‘rst’, ‘md’, ‘html’, ‘LaTeX’; if default value depends on the reference style (if not set in the constructor)
  • version – version of the PyMICE library to be referenced; None if no version shall be referenced
Returns:

the in-text reference
Return type:

unicode

Example:

>>> citation = Citation()
>>> print(reference.cite(version='0.2.3'))
PyMICE (Dzik, Puścian, et al. 2017) v. 0.2.3 (Dzik, Łęski, & Puścian 2016)

Warning

All constructor parameters shall be given as keyword arguments.

PAPER

A bibliography entry for the paper introducing the PyMICE library.

Example:

>>> citation = Citation()
>>> print('''Bibliography:
...
... {reference.PAPER}
... '''.format(reference=citation))
Bibliography:

Dzik J. M., Puścian A., Mijakowska Z., Radwanska K., Łęski S. (June 22, 2017)
    "PyMICE: A Python library for analysis of IntelliCage data" Behavior
    Research Methods doi: 10.3758/s13428-017-0907-5
Type:unicode
referencePaper(style=None, **kwargs)

Generete a bibliography entry for the paper introducing the PyMICE library. Keyword attributes override parameters set in the object constructor.

Keyword Arguments:
 
  • style – reference style; must be one of ‘PyMICE’, ‘APA6’, ‘Vancouver’, ‘BibTeX’
  • markdown – markdown language to be used; must be one of ‘txt’, ‘rst’, ‘md’, ‘html’, ‘LaTeX’
Returns:

the bibliography entry
Return type:

unicode

Example:

>>> citation = Citation()
>>> print('''Bibliography:
...
... {reference}
... '''.format(reference=citation.referencePaper(style='Vancouver',
...                                              markdown='HTML')))
Bibliography:

1. Dzik&nbsp;JM, Puścian&nbsp;A, Mijakowska&nbsp;Z, Radwanska&nbsp;K,
    Łęski&nbsp;S. PyMICE: A Python library for analysis of IntelliCage data.
    Behav Res Methods. 2017. DOI:&nbsp;10.3758/s13428-017-0907-5

Warning

All constructor parameters shall be given as keyword arguments.

SOFTWARE

A bibliography entry for the PyMICE library.

Example:

>>> citation = Citation(version='1.1.1')
>>> print('''Bibliography:
...
... {reference.SOFTWARE}
... '''.format(reference=citation))
Bibliography:

Dzik J. M., Łęski S., Puścian A. (April 24, 2017) "PyMICE" computer software
    (v. 1.1.1; RRID:nlx_158570) doi: 10.5281/zenodo.557087
Type:unicode
referenceSoftware(style=None, **kwargs)

Generete a bibliography entry for the PyMICE library. Keyword attributes override parameters set in the object constructor.

Keyword Arguments:
 
  • style – reference style; must be one of ‘PyMICE’, ‘APA6’, ‘Vancouver’, ‘BibTeX’
  • markdown – markdown language to be used; must be one of ‘txt’, ‘rst’, ‘md’, ‘html’, ‘LaTeX’; if default value depends on the reference style (if not set in the constructor)
  • version – version of the PyMICE library to be referenced; None if no version shall be referenced
Returns:

the bibliography entry
Return type:

unicode

Example:

>>> citation = Citation()
>>> print(citation.referenceSoftware(style='BibTeX',
...                                  version='1.0.0'))
@Misc{pymice1.0.0,
Title = {{PyMICE (v.~1.0.0)}},
Note = {computer software; RRID:nlx\_158570},
Author = {Dzik, Jakub Mateusz and Łęski, Szymon and Puścian, Alicja},
Year = {2016},
Month = {May},
Day = {6},
Doi = {10.5281/zenodo.51092}
}

Warning

All constructor parameters shall be given as keyword arguments.

CITE_PAPER

A prefabricated stem of an in-text reference of the paper introducing the PyMICE library.

Type:unicode
citePaper(style=None, **kwargs)

Prefabricate the stem of an in-text reference to the publication introducing the PyMICE library. Keyword attributes override parameters set in the object constructor.

Keyword Arguments:
 
  • style – reference style; must be one of ‘PyMICE’, ‘APA6’, ‘Vancouver’, ‘BibTeX’
  • markdown – markdown language to be used; must be one of ‘txt’, ‘rst’, ‘md’, ‘html’, ‘LaTeX’; if default value depends on the reference style (if not set in the constructor)
Returns:

the prefabricated reference stem
Return type:

unicode

Example:

>>> citation = Citation()
>>> print('''The library has been introduced in our paper~\\cite{{{}}},
... so we ask that reference to the paper is provided in any published
... research making use of PyMICE.
... '''.format(reference.citePaper(markdown='LaTeX')))
The library has been introduced in our paper~\cite{dzik2017pm},
so we ask that reference to the paper is provided in any published
research making use of PyMICE.

Warning

All constructor parameters shall be given as keyword arguments.

CITE_SOFTWARE

A prefabricated stem of an in-text reference of the PyMICE library.

Type:unicode
citeSoftware(style=None, **kwargs)

Prefabricate the stem of an in-text reference to the PyMICE library. Keyword attributes override parameters set in the object constructor.

Keyword Arguments:
 
  • style – reference style; must be one of ‘PyMICE’, ‘APA6’, ‘Vancouver’, ‘BibTeX’
  • markdown – markdown language to be used; must be one of ‘txt’, ‘rst’, ‘md’, ‘html’, ‘LaTeX’; if default value depends on the reference style (if not set in the constructor)
  • version – version of the PyMICE library to be referenced; None if no version shall be referenced
Returns:

the prefabricated reference stem
Return type:

unicode

Example:

>>> citation = Citation()
>>> print(reference.citeSoftware(version='1.1.1', style='APA6'))
Dzik, Łęski, & Puścian, 2017

Warning

All constructor parameters shall be given as keyword arguments.

Module pymice.debug

A collection of auxilary validation tools for PyMICE library.

pymice.debug.plotPhases(timeline, tzone=None, ax=None)

Plot a diagnostic plot of phases of the experiment timeline.

Parameters:
  • timeline (pymice.ExperimentTimeline) – the timeline
  • tzone (datetime.tzinfo or None) – timezone of the plot or None
  • ax (matplotlib.axes.Axes or None) – axis or None
Returns:

a new figure if ax parameter not provided else None
Return type:

matplotlib.figure.Figure or None